Hunger, for one thing. When I'm underground, building for hours (real life) I don't like to have to carry some food with me, to not die from every small fall because hunger reduced my health to half a heart. I don't see the need for experience points in a game which, to me at least, is about constructing interesting stuff. Same goes for the End and the fighting system. And from the newer changes I don't really like the Villages and such. I don't know, I feel it just pushed the game in the wrong direction. Yes, the introduction of the Creative mode, was good, but I liked the "survival building" aspect. I would love to have a classic "survival" mode in addition to Creative and Adventure, but that's probably not going to happen.
Edit: and I almost forgot the fucking chests. These fucking chests. Blocks are supposed to be one block wide and long. That is so fucking annoying.